rs10512425

Positions:

• chr17-20720675-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_172472.1(LOC100287072):​n.1262+90G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 591,848 control chromosomes in the GnomAD database, including 1,053 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.051 (214 hom., cov: 31)
  • Exomes 𝑓: 0.057 (839 hom.)
• Consequence: LOC100287072 NR_172472.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100287072	NR_172472.1	n.1262+90G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000441215.2	n.203+90G>C		intron_variant, non_coding_transcript_variant
	ENST00000578210.5	n.205+90G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7779 AN: 152102 Hom.: 214 Cov.: 31

Gnomad AFR AF: 0.0355

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0443

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0564

GnomAD4 exome AF: 0.0569 AC: 25003 AN: 439628 Hom.: 839 AF XY: 0.0559 AC XY: 13595 AN XY: 243304

Gnomad4 AFR exome AF: 0.0333

Gnomad4 AMR exome AF: 0.0899

Gnomad4 ASJ exome AF: 0.0618

Gnomad4 EAS exome AF: 0.0158

Gnomad4 SAS exome AF: 0.0445

Gnomad4 FIN exome AF: 0.0451

Gnomad4 NFE exome AF: 0.0632

Gnomad4 OTH exome AF: 0.0519

GnomAD4 genome AF: 0.0511 AC: 7784 AN: 152220 Hom.: 214 Cov.: 31 AF XY: 0.0502 AC XY: 3737 AN XY: 74434

Gnomad4 AFR AF: 0.0356

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0440

Gnomad4 FIN AF: 0.0443

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0627 Hom.: 53

Bravo AF: 0.0514

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10512425; hg19: chr17-20623988;